Résumé
Rapidly growing biological data –including molecular sequences and
fossils– hold an unprecedented potential to reveal how evolutionary
processes generate and maintain biodiversity. However, researchers often
have to develop their own idiosyncratic workflows to integrate and analyse
these data for reconstructing time-calibrated phylogenies. In addition,
divergence times estimated under different methods and assumptions, and
based on data of various quality and reliability, should not be combined
without proper correction. Here we introduce a modular framework termed
SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and
Migration, Ages, and Relationships of Taxa), and provide a proof of
concept for dealing with the moving targets of evolutionary and
biogeographical research. This framework assembles comprehensive datasets
of molecular and fossil data for any taxa and infers dated phylogenies
using robust species tree methods, also allowing for the inclusion of
genomic data produced through next-generation sequencing techniques. We
exemplify the application of our method by presenting phylogenetic and
dating analyses for the mammal order Primates and for the plant family
Arecaceae (palms). We believe that this framework will provide a valuable
tool for a wide range of hypothesis-driven research questions in
systematics, biogeography, and evolution. SUPERSMART will also accelerate
the inference of a “Dated Tree of Life” where all node ages are directly
comparable.